Prefer bcftools/liftover

Author: bbimber

mGAP/src/org/labkey/mgap/pipeline/AnnotationStep.java

@@ -31,6 +31,7 @@
 import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStep;
 import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStepOutputImpl;
 import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep;
+import org.labkey.api.sequenceanalysis.run.LiftoverBcfToolsWrapper;
 import org.labkey.api.sequenceanalysis.run.SelectVariantsWrapper;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.writer.PrintWriters;
@@ -327,8 +328,8 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
         File liftoverRejects = new File(outputDirectory, SequenceAnalysisService.get().getUnzippedBaseName(currentVcf.getName()) + ".liftoverReject" + grch37Genome.getGenomeId() + ".vcf.gz");
         if (!indexExists(liftoverRejects) || !indexExists(liftedToGRCh37))
         {
-            LiftoverVcfRunner liftoverVcfRunner = new LiftoverVcfRunner(getPipelineCtx().getLogger());
-            liftoverVcfRunner.doLiftover(currentVcf, chainFile, grch37Genome.getWorkingFastaFile(), liftoverRejects, liftedToGRCh37, 0.95);
+            LiftoverBcfToolsWrapper liftoverVcfRunner = new LiftoverBcfToolsWrapper(getPipelineCtx().getLogger());
+            liftoverVcfRunner.doLiftover(currentVcf, chainFile, genome.getWorkingFastaFile(), grch37Genome.getWorkingFastaFile(), liftoverRejects, liftedToGRCh37);
         }
         else
         {

mGAP/src/org/labkey/mgap/pipeline/LiftoverVcfRunner.java

@@ -31,7 +31,6 @@
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.exp.api.ExperimentService;
-import org.labkey.api.jbrowse.JBrowseService;
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
@@ -56,6 +55,7 @@
 import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
 import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor;
 import org.labkey.api.sequenceanalysis.run.GeneToNameTranslator;
+import org.labkey.api.sequenceanalysis.run.LiftoverBcfToolsWrapper;
 import org.labkey.api.sequenceanalysis.run.SelectVariantsWrapper;
 import org.labkey.api.util.FileType;
 import org.labkey.api.util.FileUtil;
@@ -77,7 +77,6 @@
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
-import java.util.Comparator;
 import java.util.Date;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -1024,7 +1023,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
 
             File sitesOnlyVcf = getSitesOnlyVcf(ctx, primaryTrackVcf, genome);
 
-            File lifted = liftToHuman(ctx, primaryTrackVcf, sitesOnlyVcf, grch37Genome);
+            File lifted = liftToHuman(ctx, primaryTrackVcf, sitesOnlyVcf, genome, grch37Genome);
             SequenceOutputFile output3 = new SequenceOutputFile();
             output3.setFile(lifted);
             output3.setName("mGAP Release: " + species + " " + releaseVersion + " Lifted to Human");
@@ -1095,7 +1094,7 @@ private File getSitesOnlyVcf(JobContext ctx, File primaryTrackVcf, ReferenceGeno
             return noGenotypes;
         }
 
-        private File liftToHuman(JobContext ctx, File primaryTrackVcf, File noGenotypes, ReferenceGenome grch37Genome) throws PipelineJobException
+        private File liftToHuman(JobContext ctx, File primaryTrackVcf, File noGenotypes, ReferenceGenome sourceGenome, ReferenceGenome grch37Genome) throws PipelineJobException
         {
             //lift to target genome
             Integer chainFileId = ctx.getSequenceSupport().getCachedObject(AnnotationStep.CHAIN_FILE, Integer.class);
@@ -1108,8 +1107,8 @@ private File liftToHuman(JobContext ctx, File primaryTrackVcf, File noGenotypes,
             File liftoverRejects = new File(ctx.getOutputDir(), SequenceAnalysisService.get().getUnzippedBaseName(primaryTrackVcf.getName()) + ".liftoverRejectGRCh37.vcf.gz");
             if (!indexExists(liftoverRejects))
             {
-                LiftoverVcfRunner liftoverVcfRunner = new LiftoverVcfRunner(ctx.getLogger());
-                liftoverVcfRunner.doLiftover(noGenotypes, chainFile, grch37Genome.getWorkingFastaFile(), liftoverRejects, liftedToGRCh37, 0.95);
+                LiftoverBcfToolsWrapper liftoverVcfRunner = new LiftoverBcfToolsWrapper(ctx.getLogger());
+                liftoverVcfRunner.doLiftover(noGenotypes, chainFile, sourceGenome.getWorkingFastaFile(), grch37Genome.getWorkingFastaFile(), liftoverRejects, liftedToGRCh37);
             }
             else
             {

mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java

@@ -83,7 +83,7 @@ public SequenceOutputProcessor getProcessor()
         return new Processor();
     }
 
-    public class Processor implements SequenceOutputProcessor
+    public static class Processor implements SequenceOutputProcessor
     {
         @Override
         public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport support, List<SequenceOutputFile> inputFiles, JSONObject params, File outputDir, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException

primeseq/src/org/labkey/primeseq/analysis/CombineMethylationRatesHandler.java

@@ -172,7 +172,7 @@ public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport
                 Map<String, SequenceOutputFile> fileMap = new HashMap<>();
                 for (SequenceOutputFile f : inputFiles)
                 {
-                    action.addInputIfNotPresent(f.getFile(), "Methlylation Rates");
+                    action.addInputIfNotPresent(f.getFile(), "Methylation Rates");
                     fileMap.put(f.getRowid().toString(), f);
                 }